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Literature DB >> 14759262

Versatile and open software for comparing large genomes.

Stefan Kurtz¹, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg.

Abstract

The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer.

Entities: Disease Gene Species

Mesh：

Year: 2004 PMID： 14759262 PMCID： PMC395750 DOI： 10.1186/gb-2004-5-2-r12

Source DB: PubMed Journal: Genome Biol ISSN： 1474-7596 Impact factor: 13.583

28 in total

1. CAP3: A DNA sequence assembly program.

Authors: X Huang; A Madan
Journal: Genome Res Date: 1999-09 Impact factor: 9.043

2. Flexible sequence similarity searching with the FASTA3 program package.

Authors: W R Pearson
Journal: Methods Mol Biol Date: 2000

3. REPuter: the manifold applications of repeat analysis on a genomic scale.

Authors: S Kurtz; J V Choudhuri; E Ohlebusch; C Schleiermacher; J Stoye; R Giegerich
Journal: Nucleic Acids Res Date: 2001-11-15 Impact factor: 16.971

4. SSAHA: a fast search method for large DNA databases.

Authors: Z Ning; A J Cox; J C Mullikin
Journal: Genome Res Date: 2001-10 Impact factor: 9.043

5. Fast algorithms for large-scale genome alignment and comparison.

Authors: Arthur L Delcher; Adam Phillippy; Jane Carlton; Steven L Salzberg
Journal: Nucleic Acids Res Date: 2002-06-01 Impact factor: 16.971

6. Efficient multiple genome alignment.

Authors: Michael Höhl; Stefan Kurtz; Enno Ohlebusch
Journal: Bioinformatics Date: 2002 Impact factor: 6.937

7. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.

Authors: Evgeny M Zdobnov; Christian von Mering; Ivica Letunic; David Torrents; Mikita Suyama; Richard R Copley; George K Christophides; Dana Thomasova; Robert A Holt; G Mani Subramanian; Hans-Michael Mueller; George Dimopoulos; John H Law; Michael A Wells; Ewan Birney; Rosane Charlab; Aaron L Halpern; Elena Kokoza; Cheryl L Kraft; Zhongwu Lai; Suzanna Lewis; Christos Louis; Carolina Barillas-Mury; Deborah Nusskern; Gerald M Rubin; Steven L Salzberg; Granger G Sutton; Pantelis Topalis; Ron Wides; Patrick Wincker; Mark Yandell; Frank H Collins; Jose Ribeiro; William M Gelbart; Fotis C Kafatos; Peer Bork
Journal: Science Date: 2002-10-04 Impact factor: 47.728

8. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.

Authors: Timothy D Read; Steven L Salzberg; Mihai Pop; Martin Shumway; Lowell Umayam; Lingxia Jiang; Erik Holtzapple; Joseph D Busch; Kimothy L Smith; James M Schupp; Daniel Solomon; Paul Keim; Claire M Fraser
Journal: Science Date: 2002-05-09 Impact factor: 47.728

9. ARACHNE: a whole-genome shotgun assembler.

Authors: Serafim Batzoglou; David B Jaffe; Ken Stanley; Jonathan Butler; Sante Gnerre; Evan Mauceli; Bonnie Berger; Jill P Mesirov; Eric S Lander
Journal: Genome Res Date: 2002-01 Impact factor: 9.043

10. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.

Authors: R D Fleischmann; D Alland; J A Eisen; L Carpenter; O White; J Peterson; R DeBoy; R Dodson; M Gwinn; D Haft; E Hickey; J F Kolonay; W C Nelson; L A Umayam; M Ermolaeva; S L Salzberg; A Delcher; T Utterback; J Weidman; H Khouri; J Gill; A Mikula; W Bishai; W R Jacobs; J C Venter; C M Fraser
Journal: J Bacteriol Date: 2002-10 Impact factor: 3.490

2000 in total

1. Evolutionary dynamics of bacteria in a human host environment.

Authors: Lei Yang; Lars Jelsbak; Rasmus Lykke Marvig; Søren Damkiær; Christopher T Workman; Martin Holm Rau; Susse Kirkelund Hansen; Anders Folkesson; Helle Krogh Johansen; Oana Ciofu; Niels Høiby; Morten O A Sommer; Søren Molin
Journal: Proc Natl Acad Sci U S A Date: 2011-04-25 Impact factor: 11.205

2. Bulk segregant analysis followed by high-throughput sequencing reveals the Neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1.

Authors: Kyle R Pomraning; Kristina M Smith; Michael Freitag
Journal: Eukaryot Cell Date: 2011-04-22

3. Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus.

Authors: Stephen B Beres; Ellen W Richter; Michal J Nagiec; Paul Sumby; Stephen F Porcella; Frank R DeLeo; James M Musser
Journal: Proc Natl Acad Sci U S A Date: 2006-04-24 Impact factor: 11.205

4. SssP1, a Streptococcus suis Fimbria-Like Protein Transported by the SecY2/A2 System, Contributes to Bacterial Virulence.

Authors: Yue Zhang; Pengpeng Lu; Zihao Pan; Yinchu Zhu; Jiale Ma; Xiaojun Zhong; Wenyang Dong; Chengping Lu; Huochun Yao
Journal: Appl Environ Microbiol Date: 2018-08-31 Impact factor: 4.792

5. Human Infections Caused by Clonally Related African Clade (Clade III) Strains of Candida auris in the Greater Houston Region.

Authors: S Wesley Long; Matthew Ojeda Saavedra; Paul A Christensen; James M Musser; Randall J Olsen
Journal: J Clin Microbiol Date: 2020-06-24 Impact factor: 5.948

6. Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production.

Authors: Chinae Thammarongtham; Intawat Nookaew; Tayvich Vorapreeda; Tanawut Srisuk; Miriam L Land; Sukanya Jeennor; Kobkul Laoteng
Journal: Curr Microbiol Date: 2017-09-01 Impact factor: 2.188

7. Helicobacter pullorum isolated from fresh chicken meat: antibiotic resistance and genomic traits of an emerging foodborne pathogen.

Authors: Vítor Borges; Andrea Santos; Cristina Belo Correia; Margarida Saraiva; Armelle Ménard; Luís Vieira; Daniel A Sampaio; Miguel Pinheiro; João Paulo Gomes; Mónica Oleastro
Journal: Appl Environ Microbiol Date: 2015-09-18 Impact factor: 4.792